Computational Simulation Study On The Binding And Selectivity Mechanism Of Negative Allosteric Modulators In Group ? Metabotropic Glutamate Receptors

Metabotropic glutamate receptors?mGluRs?,belonging to the class C G-protein-coupled receptors?GPCRs?family,are promising targets for treating many psychiatric and neurodegenerative disorders.mGluRs contain a total of 8 subtypes(mGluR_1-8),according to their biochemical,structural and pharmacological properties,the eight members of mGluRs were divided into three groups:group?(mGlu_1/5),group?(mGlu_2/3)and group?(mGlu_4/6/7/8).Currently,group I mGluRs are at the forefront of research,and several negative allosteric modulators?NAMs?show excellent therapeutic activity in many preclinical and clinical studies.Such as the NAM dipraglurant targeting mGluR₅ was approved by Food and Drug Administration?FDA?for the treatment of PD-LID.In the meantime,many allosteric drug candidates negatively modulating mGluR₅ were advanced into clinical development.However,none of NAMs targerting mGluR₁ have been reached clinical study so far,and the absence of binding mode between NAMs and mGluR₁limited the drug discovery.Moreover,mGluR5 and mGluR1 belong to group I mGluRs,which have high sequence similarity as 78.5%,and pose a challenge for the initial lead compounds design and how to optimize the selectivity between the drug and the target during the successful development of the drug molecules.This work reveals the binding mechanism of different NAMs binding to the allosteric sites of mGluR₅ and mGluR₁,and explores the subtype-selectivity between the two highly conserved receptors by combining various computational methods,including docking,molecular dynamics simulation?MD?,binding free energy calculation,drug-target interaction fingerprint analysis and pharmacophore model.This study aims to provide information for the design of novel NAMs,and the main research content includes the following three parts:1.The study on the binding mode of NAMs and mGluR5.In order to comprehensively investigate the binding mechanism of NAMs binding in mGluR5,we have selected 5 clinically NAMs?mavoglurant,dipraglurant,basimglurant,STX107,and fenobam?as representative.Firstly,docking has been utilized to predict the initial receptor-ligand poses.Then,the molecular dynamics simulation and the binding free energy prediction were performed.The accuracy of the model has been verified by in silico site-directed mutagenesis analysis and the correlation between calculated and experimental values.Moreover,11 residues(I625^2.46,I651^3.36,S654^3.39,P655^3.40,L744^5.44,W785^6.50,F788^6.53,M802^7.32,V806^7.36,S809⁷.39.39 and A810^7.40)in mGluR₅ have been identified by per-residue binding free energy contribution analysis to play a vital role in the common mode of NAMs binding to mGluR₅.2.The study on the binding mode of NAMs and mGluR1.The binding mode of NAMs in mGluR₁ has been explored by the aforementioned methods based on 4selective mGluR₁ NAMs.As a result,6“Hot Spots”(N760^5.47,F801^6.53,L757^5.44,V664^3.36,T815^7.32,V753^5.40)and 11“Warm Spots”residues(L648^2.56,R661^3.33,G665^3.37,S668^3.40,T748^ECL2,P756^5.43,I797^6.49,W798^6.50,I812^7.29,A818^7.35 and V819^7.36)have been identified.Finally,the detailed binding mode of NAMs in mGluR₁ and the molecular mechanism of analogs bingding to mGluR₁ with different affinities were revealed.3.The study on the subtype selectivity of mGluR5 versus mGluR1.The drug targeting and safety are based on the drug selectivity,which has gained widespread attention in the drug design.The mGluR₅ and mGluR₁ belonging to Group?mGluRs shared high sequence identity,and drug selectivity is very important to mGluR₅ and mGluR₁.In this work,the selective mechanism between mGluR₅ and mGluR₁ has been revealed in terms of energy contributions,binding poses,and ligand-protein interactions fingerprint analysis.As a result,9 residues including 6 non-conservative residues(mGluR₅:I651^3.36,P655^3.40,S658^3.43,M802^7.32,S805^7.35,A810^7.40,mGluR₁:V664^3.36,S668^3.40,C671^3.43,T815^7.32,A818^7.35,V823^7.40)and 3 conservative residues(mGluR₅:L744^5.44,N747^5.47,W785^6.50,mGluR₁:L757^5.44,N760^5.47,W798^6.50)were identified as important features to control the NAMs binding selectivity in the two receptors.In summary,this study reveales the detail binding mechanism of different NAMs binding to group I mGluRs,and further identifies the selective characteristics between these two receptors to provide a theoretical basis for further expanding the compound skeleton and developing new NAMs with excellent selectivity,affinity.This work also provides new methods and strategies for the development of drugs for psychiatric and neurodegenerative disorders affecting the quality of human life seriously.